Quantitative trait loci for the number of vertebrae on Sus scrofa chromosomes 1 and 7 independently influence the numbers of thoracic and lumbar vertebrae in pigs

doi:10.1016/S2095-3119(15)61084-X

Journal of Integrative Agriculture ›› 2015, Vol. 14 ›› Issue (10): 2027-2033.DOI: 10.1016/S2095-3119(15)61084-X

Quantitative trait loci for the number of vertebrae on Sus scrofa chromosomes 1 and 7 independently influence the numbers of thoracic and lumbar vertebrae in pigs

ZHANG Long-chao, LIU Xin, LIANG Jing, YAN Hua, ZHAO Ke-bin, LI Na, PU Lei, SHI Hui-bi, ZHANG Yue-bo, WANG Li-gang, WANG Li-xian

Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation, Ministry of Agriculture/Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China Abstract

收稿日期:2015-03-31 出版日期:2015-10-09 发布日期:2015-10-12
通讯作者: WANG Li-xian, Tel: +86-10-62818771,E-mail: iaswlx@263.net; WANG Li-gang, Tel: +86-10-62816011,E-mail: ligwang@126.com
作者简介:Zhang Long-chao, Tel: +86-10-62816011, E-mail: zhlchias@163.com; LIU Xin, Tel: +86-10-62816011, E-mail: firstliuxin@163.com;* These authors contributed equally to this study.
基金资助:
This research was supported by the Agricultural Science and Technology Innovation Program, China (ASTIP-IAS02), the National Key Technology R&D Program of China (2011BAD28B01), the National Natural Science Foundation of China (31201781), the Earmarked Fund for Modern Agro-Industry Technology Research System, the National Key Technology R&D Program of China (2011ZX08006-003) and the Chinese Academy of Agricultural Sciences Foundation (2014ZL006, 2011cj-5, 2012ZL069 and 2014ywf-yb-8).

Quantitative trait loci for the number of vertebrae on Sus scrofa chromosomes 1 and 7 independently influence the numbers of thoracic and lumbar vertebrae in pigs

ZHANG Long-chao, LIU Xin, LIANG Jing, YAN Hua, ZHAO Ke-bin, LI Na, PU Lei, SHI Hui-bi, ZHANG Yue-bo, WANG Li-gang, WANG Li-xian

Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation, Ministry of Agriculture/Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China Abstract

Received:2015-03-31 Online:2015-10-09 Published:2015-10-12
Contact: WANG Li-xian, Tel: +86-10-62818771,E-mail: iaswlx@263.net; WANG Li-gang, Tel: +86-10-62816011,E-mail: ligwang@126.com
About author:Zhang Long-chao, Tel: +86-10-62816011, E-mail: zhlchias@163.com; LIU Xin, Tel: +86-10-62816011, E-mail: firstliuxin@163.com;* These authors contributed equally to this study.
Supported by:
This research was supported by the Agricultural Science and Technology Innovation Program, China (ASTIP-IAS02), the National Key Technology R&D Program of China (2011BAD28B01), the National Natural Science Foundation of China (31201781), the Earmarked Fund for Modern Agro-Industry Technology Research System, the National Key Technology R&D Program of China (2011ZX08006-003) and the Chinese Academy of Agricultural Sciences Foundation (2014ZL006, 2011cj-5, 2012ZL069 and 2014ywf-yb-8).

摘要/Abstract

摘要： Although quantitative trait loci (QTLs) for number of thoracic-lumbar vertebrae have been identified on Sus scrofa chromosomes (SSCs) 1 and 7, the influence of these QTLs on the thoracic and lumbar vertebrae is not clear. The aim of this study was to identify single nucleotide polymorphisms (SNPs) associated with total number of thoracic-lumbar vertebrae and for each trait (number of thoracic and lumbar vertebrae) separately. A total of 581 individuals from an F2 Large White×Minzhu population were genotyped using an SNP60K chip. Performing a genome-wide association study (GWAS) for total number of thoracic-lumbar vertebrae, 38 significant SNPs were identified in two QTL regions located on SSC1 and SSC7. Performing a GWAS for number of thoracic vertebrae only, 72 significant SNPs were located on SSC7. While performing a GWAS for number of lumbar vertebrae only, 17 significant SNPs were identified on SSC1. Gene mining suggested that the gene encoding orphan nuclear receptor, germ cell nuclear factor (NR6A1) on SSC1 was a strong candidate affecting the number of lumbar vertebrae in pigs. Additionally, genes encoding vertnin (VRTN), prospero homeobox 2 (PROX2), Finkel-Biskis-Jinkins murine osteosarcoma viral oncogene homolog (FOS), and transforming growth factor beta 3 (TGFB3) may be important candidates affecting the number of thoracic vertebrae in pigs. QTLs on SSC1 and SSC7 independently influenced the numbers of thoracic and lumbar vertebrae. These results shed light on the complex genetic background of vertebrae development in pigs.

关键词: candidate gene , genetic variant , genome-wide association study , number of vertebrae , pig , QTLs

Abstract: Although quantitative trait loci (QTLs) for number of thoracic-lumbar vertebrae have been identified on Sus scrofa chromosomes (SSCs) 1 and 7, the influence of these QTLs on the thoracic and lumbar vertebrae is not clear. The aim of this study was to identify single nucleotide polymorphisms (SNPs) associated with total number of thoracic-lumbar vertebrae and for each trait (number of thoracic and lumbar vertebrae) separately. A total of 581 individuals from an F2 Large White×Minzhu population were genotyped using an SNP60K chip. Performing a genome-wide association study (GWAS) for total number of thoracic-lumbar vertebrae, 38 significant SNPs were identified in two QTL regions located on SSC1 and SSC7. Performing a GWAS for number of thoracic vertebrae only, 72 significant SNPs were located on SSC7. While performing a GWAS for number of lumbar vertebrae only, 17 significant SNPs were identified on SSC1. Gene mining suggested that the gene encoding orphan nuclear receptor, germ cell nuclear factor (NR6A1) on SSC1 was a strong candidate affecting the number of lumbar vertebrae in pigs. Additionally, genes encoding vertnin (VRTN), prospero homeobox 2 (PROX2), Finkel-Biskis-Jinkins murine osteosarcoma viral oncogene homolog (FOS), and transforming growth factor beta 3 (TGFB3) may be important candidates affecting the number of thoracic vertebrae in pigs. QTLs on SSC1 and SSC7 independently influenced the numbers of thoracic and lumbar vertebrae. These results shed light on the complex genetic background of vertebrae development in pigs.

Key words: candidate gene , genetic variant , genome-wide association study , number of vertebrae , pig , QTLs

ZHANG Long-chao, LIU Xin, LIANG Jing, YAN Hua, ZHAO Ke-bin, LI Na, PU Lei, SHI Hui-bi, ZHANG Yue-bo, WANG Li-gang, WANG Li-xian. Quantitative trait loci for the number of vertebrae on Sus scrofa chromosomes 1 and 7 independently influence the numbers of thoracic and lumbar vertebrae in pigs[J]. Journal of Integrative Agriculture, 2015, 14(10): 2027-2033.

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Quantitative trait loci for the number of vertebrae on Sus scrofa chromosomes 1 and 7 independently influence the numbers of thoracic and lumbar vertebrae in pigs

Quantitative trait loci for the number of vertebrae on Sus scrofa chromosomes 1 and 7 independently influence the numbers of thoracic and lumbar vertebrae in pigs

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